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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.25

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-11-07, 09:39 CET based on data in: /DKHC/scratch/markop/_p_Endophytes/_I_Bsubtilis/_S_NGS_monocultures/_A_RNAseq-STAR_limma/output


        General Statistics

        Showing 0/144 rows and 9/16 columns.
        Sample NameTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedTrimmed bases% Solanum tuberosum% Top 5 Species% UnclassifiedDupsGCAvg lenMedian lenFailedSeqs
        BS443
        21.9M
        20.0M
        91.4%
        19.0M
        86.9%
        1.0M
        BS443_1
        0.6%
        88.2%
        43.0%
        150bp
        150bp
        9%
        21.9M
        BS443_2
        0.6%
        87.5%
        44.0%
        150bp
        150bp
        9%
        21.9M
        BS444
        19.8M
        18.3M
        92.4%
        17.4M
        88.1%
        0.9M
        BS444_1
        0.6%
        81.6%
        43.0%
        150bp
        150bp
        9%
        19.8M
        BS444_2
        0.6%
        81.0%
        44.0%
        150bp
        150bp
        9%
        19.8M
        BS445
        21.6M
        19.9M
        92.3%
        19.0M
        88.1%
        0.9M
        BS445_1
        0.5%
        80.6%
        43.0%
        150bp
        150bp
        9%
        21.6M
        BS445_2
        0.6%
        79.2%
        43.0%
        150bp
        150bp
        9%
        21.6M
        BS446
        20.2M
        18.4M
        91.0%
        17.5M
        86.9%
        0.8M
        BS446_1
        0.5%
        78.7%
        42.0%
        150bp
        150bp
        9%
        20.2M
        BS446_2
        0.6%
        78.0%
        43.0%
        150bp
        150bp
        9%
        20.2M
        BS447
        22.2M
        19.9M
        89.5%
        18.4M
        83.0%
        1.5M
        BS447_1
        0.6%
        90.6%
        44.0%
        150bp
        150bp
        9%
        22.2M
        BS447_2
        0.6%
        89.9%
        44.0%
        150bp
        150bp
        9%
        22.2M
        BS448
        23.4M
        21.1M
        90.0%
        20.1M
        85.6%
        1.0M
        BS448_1
        0.6%
        89.6%
        43.0%
        150bp
        150bp
        9%
        23.4M
        BS448_2
        0.7%
        89.0%
        44.0%
        150bp
        150bp
        9%
        23.4M
        BS449
        24.5M
        20.6M
        84.2%
        19.3M
        78.8%
        1.3M
        BS449_1
        0.7%
        95.1%
        44.0%
        150bp
        150bp
        9%
        24.5M
        BS449_2
        0.8%
        94.4%
        45.0%
        150bp
        150bp
        9%
        24.5M
        BS450
        23.4M
        19.0M
        81.2%
        17.9M
        76.5%
        1.1M
        BS450_1
        0.7%
        95.7%
        45.0%
        150bp
        150bp
        9%
        23.5M
        BS450_2
        0.8%
        95.0%
        45.0%
        150bp
        150bp
        9%
        23.5M
        BS451
        23.8M
        19.1M
        80.3%
        18.1M
        76.2%
        1.0M
        BS451_1
        0.7%
        89.8%
        44.0%
        150bp
        150bp
        9%
        23.8M
        BS451_2
        0.8%
        88.6%
        44.0%
        150bp
        150bp
        9%
        23.8M
        BS452
        21.5M
        18.2M
        84.3%
        17.2M
        79.8%
        1.0M
        BS452_1
        0.6%
        94.1%
        43.0%
        150bp
        150bp
        9%
        21.5M
        BS452_2
        0.7%
        92.5%
        44.0%
        150bp
        150bp
        9%
        21.5M
        BS453
        23.1M
        18.2M
        78.9%
        17.2M
        74.7%
        1.0M
        BS453_1
        0.7%
        93.5%
        45.0%
        150bp
        150bp
        9%
        23.1M
        BS453_2
        0.7%
        92.7%
        46.0%
        150bp
        150bp
        18%
        23.1M
        BS454
        22.2M
        18.9M
        85.3%
        17.9M
        80.8%
        1.0M
        BS454_1
        0.7%
        94.2%
        43.0%
        150bp
        150bp
        9%
        22.2M
        BS454_2
        0.7%
        93.3%
        44.0%
        150bp
        150bp
        9%
        22.2M
        BS463
        21.6M
        18.2M
        83.9%
        17.3M
        80.0%
        0.8M
        BS463_1
        0.6%
        91.6%
        45.0%
        150bp
        150bp
        9%
        21.7M
        BS463_2
        0.6%
        90.7%
        45.0%
        150bp
        150bp
        18%
        21.7M
        BS464
        24.2M
        19.9M
        82.4%
        18.9M
        78.1%
        1.0M
        BS464_1
        0.6%
        94.2%
        44.0%
        150bp
        150bp
        9%
        24.2M
        BS464_2
        0.7%
        93.3%
        44.0%
        150bp
        150bp
        9%
        24.2M
        BS465
        23.7M
        22.1M
        93.2%
        20.9M
        88.3%
        1.2M
        BS465_1
        0.5%
        83.8%
        43.0%
        150bp
        150bp
        9%
        23.7M
        BS465_2
        0.6%
        82.4%
        44.0%
        150bp
        150bp
        9%
        23.7M
        BS466
        22.1M
        19.6M
        88.5%
        18.6M
        84.0%
        1.0M
        BS466_1
        0.6%
        90.7%
        43.0%
        150bp
        150bp
        9%
        22.1M
        BS466_2
        0.7%
        89.6%
        44.0%
        150bp
        150bp
        9%
        22.1M
        BS467
        23.1M
        19.5M
        84.3%
        18.6M
        80.4%
        0.9M
        BS467_1
        0.7%
        93.6%
        43.0%
        150bp
        150bp
        9%
        23.1M
        BS467_2
        0.7%
        93.1%
        44.0%
        150bp
        150bp
        9%
        23.1M
        BS468
        22.8M
        17.3M
        75.6%
        15.0M
        65.4%
        2.3M
        BS468_1
        0.7%
        95.2%
        45.0%
        150bp
        150bp
        9%
        22.9M
        BS468_2
        0.7%
        94.4%
        46.0%
        150bp
        150bp
        9%
        22.9M
        BS469
        23.5M
        21.2M
        90.1%
        20.2M
        86.1%
        0.9M
        BS469_1
        0.6%
        88.1%
        42.0%
        150bp
        150bp
        9%
        23.5M
        BS469_2
        0.6%
        87.5%
        43.0%
        150bp
        150bp
        9%
        23.5M
        BS470
        24.6M
        22.4M
        91.1%
        21.3M
        86.8%
        1.1M
        BS470_1
        0.5%
        85.1%
        42.0%
        150bp
        150bp
        9%
        24.6M
        BS470_2
        0.6%
        84.6%
        43.0%
        150bp
        150bp
        9%
        24.6M
        BS471
        21.8M
        19.1M
        87.3%
        18.2M
        83.2%
        0.9M
        BS471_1
        0.6%
        90.3%
        42.0%
        150bp
        150bp
        9%
        21.8M
        BS471_2
        0.7%
        89.6%
        43.0%
        150bp
        150bp
        9%
        21.8M
        BS472
        23.4M
        1.2M
        5.0%
        0.9M
        4.0%
        0.2M
        BS472_1
        1.2%
        97.6%
        51.0%
        150bp
        150bp
        9%
        23.4M
        BS472_2
        1.3%
        96.6%
        51.0%
        150bp
        150bp
        9%
        23.4M
        BS473
        19.9M
        16.5M
        82.9%
        14.6M
        73.3%
        1.9M
        BS473_1
        0.6%
        90.2%
        44.0%
        150bp
        150bp
        9%
        19.9M
        BS473_2
        0.6%
        89.6%
        45.0%
        150bp
        150bp
        9%
        19.9M
        BS474
        22.0M
        19.8M
        89.8%
        18.9M
        85.9%
        0.8M
        BS474_1
        0.6%
        87.1%
        42.0%
        150bp
        150bp
        9%
        22.0M
        BS474_2
        0.6%
        86.8%
        42.0%
        150bp
        150bp
        9%
        22.0M
        BS475
        23.6M
        22.1M
        93.6%
        21.0M
        89.0%
        1.1M
        BS475_1
        0.8%
        72.7%
        42.0%
        150bp
        150bp
        9%
        23.6M
        BS475_2
        0.8%
        72.3%
        43.0%
        150bp
        150bp
        9%
        23.6M
        BS476
        23.1M
        21.5M
        93.2%
        20.5M
        88.8%
        1.0M
        BS476_1
        0.7%
        65.5%
        42.0%
        150bp
        150bp
        9%
        23.1M
        BS476_2
        0.7%
        65.6%
        43.0%
        150bp
        150bp
        9%
        23.1M
        BS477
        20.1M
        18.8M
        93.9%
        18.0M
        89.8%
        0.8M
        BS477_1
        0.7%
        65.7%
        42.0%
        150bp
        150bp
        9%
        20.1M
        BS477_2
        0.7%
        65.8%
        43.0%
        150bp
        150bp
        9%
        20.1M
        BS478
        19.6M
        18.1M
        92.3%
        17.2M
        87.8%
        0.9M
        BS478_1
        0.7%
        67.6%
        42.0%
        150bp
        150bp
        9%
        19.6M
        BS478_2
        0.8%
        67.3%
        42.0%
        150bp
        150bp
        9%
        19.6M
        BS479
        20.6M
        18.8M
        91.6%
        17.9M
        87.2%
        0.9M
        BS479_1
        0.7%
        75.5%
        42.0%
        150bp
        150bp
        9%
        20.6M
        BS479_2
        0.7%
        74.7%
        42.0%
        150bp
        150bp
        9%
        20.6M
        BS480
        21.0M
        19.2M
        91.6%
        18.2M
        86.7%
        1.0M
        BS480_1
        0.8%
        83.5%
        41.0%
        150bp
        150bp
        9%
        21.0M
        BS480_2
        0.8%
        82.5%
        42.0%
        150bp
        150bp
        9%
        21.0M
        BS481
        20.9M
        19.2M
        91.6%
        18.3M
        87.3%
        0.9M
        BS481_1
        1.2%
        80.5%
        41.0%
        150bp
        150bp
        9%
        20.9M
        BS481_2
        1.2%
        79.9%
        42.0%
        150bp
        150bp
        9%
        20.9M
        BS482
        20.4M
        18.7M
        91.5%
        17.7M
        87.0%
        0.9M
        BS482_1
        1.0%
        71.8%
        41.0%
        150bp
        150bp
        9%
        20.4M
        BS482_2
        1.1%
        70.7%
        42.0%
        150bp
        150bp
        9%
        20.4M
        BS483
        24.3M
        22.3M
        91.7%
        21.2M
        87.2%
        1.1M
        BS483_1
        1.0%
        72.3%
        41.0%
        150bp
        150bp
        9%
        24.3M
        BS483_2
        1.0%
        71.5%
        41.0%
        150bp
        150bp
        9%
        24.3M
        BS484
        23.1M
        21.2M
        91.6%
        20.1M
        87.1%
        1.0M
        BS484_1
        1.5%
        77.1%
        41.0%
        150bp
        150bp
        9%
        23.1M
        BS484_2
        1.5%
        74.9%
        42.0%
        150bp
        150bp
        9%
        23.1M
        BS485
        23.6M
        21.8M
        92.4%
        20.8M
        88.3%
        1.0M
        BS485_1
        0.9%
        66.0%
        41.0%
        150bp
        150bp
        9%
        23.6M
        BS485_2
        0.9%
        64.8%
        42.0%
        150bp
        150bp
        9%
        23.6M
        BS486
        28.0M
        25.7M
        91.9%
        24.5M
        87.4%
        1.3M
        BS486_1
        1.2%
        78.8%
        41.0%
        150bp
        150bp
        9%
        28.0M
        BS486_2
        1.2%
        78.2%
        42.0%
        150bp
        150bp
        9%
        28.0M
        kreport_BS443
        79.5%
        89.0%
        1.2%
        kreport_BS444
        81.0%
        90.0%
        0.9%
        kreport_BS445
        81.1%
        90.3%
        0.9%
        kreport_BS446
        80.2%
        89.9%
        1.3%
        kreport_BS447
        74.9%
        83.7%
        1.9%
        kreport_BS448
        78.5%
        87.3%
        1.6%
        kreport_BS449
        71.7%
        80.2%
        3.0%
        kreport_BS450
        70.1%
        77.6%
        4.0%
        kreport_BS451
        69.4%
        77.9%
        4.9%
        kreport_BS452
        73.3%
        83.4%
        2.6%
        kreport_BS453
        68.1%
        76.3%
        3.7%
        kreport_BS454
        74.1%
        82.9%
        2.7%
        kreport_BS463
        72.8%
        82.0%
        3.3%
        kreport_BS464
        71.2%
        82.3%
        3.0%
        kreport_BS465
        80.7%
        89.5%
        1.0%
        kreport_BS466
        76.6%
        86.8%
        1.9%
        kreport_BS467
        72.7%
        83.1%
        2.6%
        kreport_BS468
        56.8%
        67.6%
        4.9%
        kreport_BS469
        77.2%
        87.8%
        1.4%
        kreport_BS470
        78.3%
        88.6%
        1.2%
        kreport_BS471
        75.4%
        85.8%
        2.5%
        kreport_BS472
        3.5%
        22.2%
        24.6%
        kreport_BS473
        66.3%
        76.5%
        5.1%
        kreport_BS474
        76.8%
        88.0%
        1.5%
        kreport_BS475
        82.8%
        91.6%
        0.9%
        kreport_BS476
        82.0%
        91.2%
        1.1%
        kreport_BS477
        82.3%
        91.4%
        1.0%
        kreport_BS478
        82.3%
        91.2%
        1.1%
        kreport_BS479
        82.2%
        90.8%
        1.1%
        kreport_BS480
        80.1%
        89.8%
        1.3%
        kreport_BS481
        78.8%
        89.6%
        1.2%
        kreport_BS482
        79.3%
        89.6%
        1.4%
        kreport_BS483
        79.4%
        89.9%
        1.2%
        kreport_BS484
        81.1%
        90.0%
        1.2%
        kreport_BS485
        79.7%
        90.3%
        1.2%
        kreport_BS486
        79.1%
        89.4%
        1.2%

        STAR

        Universal RNA-seq aligner.URL: https://github.com/alexdobin/STARDOI: 10.1093/bioinformatics/bts635

        Summary Statistics

        Summary statistics from the STAR alignment

        Showing 0/36 rows and 10/19 columns.
        Sample NameTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedAvg. read lenAvg. mapped lenSplicesAnnotated splicesGT/AG splicesGC/AG splicesAT/AC splicesNon-canonical splicesMismatch rateDel rateDel lenIns rateIns len
        BS443
        21.9M
        20.0M
        91.4%
        19.0M
        86.9%
        1.0M
        298.0bp
        290.3bp
        16.4M
        14.8M
        16.2M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.3bp
        0.1%
        3.0bp
        BS444
        19.8M
        18.3M
        92.4%
        17.4M
        88.1%
        0.9M
        298.0bp
        290.4bp
        15.4M
        13.9M
        15.2M
        0.1M
        0.0M
        0.0M
        0.8%
        0.1%
        3.2bp
        0.1%
        2.9bp
        BS445
        21.6M
        19.9M
        92.3%
        19.0M
        88.1%
        0.9M
        298.0bp
        290.2bp
        16.3M
        14.7M
        16.1M
        0.1M
        0.0M
        0.0M
        0.8%
        0.1%
        3.3bp
        0.1%
        3.0bp
        BS446
        20.2M
        18.4M
        91.0%
        17.5M
        86.9%
        0.8M
        298.0bp
        290.0bp
        13.9M
        12.5M
        13.8M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.2bp
        0.1%
        3.0bp
        BS447
        22.2M
        19.9M
        89.5%
        18.4M
        83.0%
        1.5M
        298.0bp
        290.8bp
        16.0M
        14.4M
        15.8M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.0bp
        0.1%
        2.9bp
        BS448
        23.4M
        21.1M
        90.0%
        20.1M
        85.6%
        1.0M
        298.0bp
        290.0bp
        17.3M
        15.6M
        17.1M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.2bp
        0.1%
        3.0bp
        BS449
        24.5M
        20.6M
        84.2%
        19.3M
        78.8%
        1.3M
        297.0bp
        290.3bp
        17.1M
        15.4M
        16.9M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.2bp
        0.1%
        3.0bp
        BS450
        23.4M
        19.0M
        81.2%
        17.9M
        76.5%
        1.1M
        297.0bp
        290.4bp
        15.9M
        14.2M
        15.7M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.0bp
        0.1%
        2.8bp
        BS451
        23.8M
        19.1M
        80.3%
        18.1M
        76.2%
        1.0M
        297.0bp
        289.9bp
        15.0M
        13.5M
        14.9M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.3bp
        0.1%
        3.1bp
        BS452
        21.5M
        18.2M
        84.3%
        17.2M
        79.8%
        1.0M
        298.0bp
        290.0bp
        14.9M
        13.4M
        14.7M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.1bp
        0.1%
        2.9bp
        BS453
        23.1M
        18.2M
        78.9%
        17.2M
        74.7%
        1.0M
        298.0bp
        289.8bp
        14.0M
        12.6M
        13.8M
        0.1M
        0.0M
        0.0M
        0.8%
        0.1%
        3.2bp
        0.1%
        3.0bp
        BS454
        22.2M
        18.9M
        85.3%
        17.9M
        80.8%
        1.0M
        297.0bp
        289.7bp
        14.2M
        12.7M
        14.1M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.1bp
        0.1%
        2.9bp
        BS463
        21.6M
        18.2M
        83.9%
        17.3M
        80.0%
        0.8M
        298.0bp
        290.8bp
        16.2M
        14.5M
        16.0M
        0.2M
        0.0M
        0.1M
        0.8%
        0.1%
        3.1bp
        0.1%
        2.8bp
        BS464
        24.2M
        19.9M
        82.4%
        18.9M
        78.1%
        1.0M
        298.0bp
        290.4bp
        16.7M
        15.0M
        16.5M
        0.2M
        0.0M
        0.1M
        0.8%
        0.1%
        3.1bp
        0.1%
        2.9bp
        BS465
        23.7M
        22.1M
        93.2%
        20.9M
        88.3%
        1.2M
        298.0bp
        291.1bp
        20.6M
        18.5M
        20.3M
        0.2M
        0.0M
        0.1M
        0.8%
        0.1%
        3.0bp
        0.1%
        2.8bp
        BS466
        22.1M
        19.6M
        88.5%
        18.6M
        84.0%
        1.0M
        298.0bp
        290.0bp
        16.1M
        14.4M
        15.9M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.3bp
        0.1%
        2.9bp
        BS467
        23.1M
        19.5M
        84.3%
        18.6M
        80.4%
        0.9M
        298.0bp
        290.1bp
        15.6M
        13.9M
        15.4M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.1bp
        0.1%
        3.0bp
        BS468
        22.8M
        17.3M
        75.6%
        15.0M
        65.4%
        2.3M
        297.0bp
        289.7bp
        10.3M
        9.1M
        10.2M
        0.1M
        0.0M
        0.0M
        0.8%
        0.1%
        3.2bp
        0.1%
        3.5bp
        BS469
        23.5M
        21.2M
        90.1%
        20.2M
        86.1%
        0.9M
        298.0bp
        290.2bp
        16.2M
        14.5M
        16.1M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.2bp
        0.1%
        3.2bp
        BS470
        24.6M
        22.4M
        91.1%
        21.3M
        86.8%
        1.1M
        298.0bp
        290.0bp
        17.4M
        15.5M
        17.2M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.3bp
        0.1%
        3.2bp
        BS471
        21.8M
        19.1M
        87.3%
        18.2M
        83.2%
        0.9M
        298.0bp
        289.6bp
        14.2M
        12.6M
        14.0M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.1bp
        0.1%
        3.0bp
        BS472
        23.4M
        1.2M
        5.0%
        0.9M
        4.0%
        0.2M
        296.0bp
        287.9bp
        0.7M
        0.6M
        0.7M
        0.0M
        0.0M
        0.0M
        0.9%
        0.1%
        3.2bp
        0.1%
        2.9bp
        BS473
        19.9M
        16.5M
        82.9%
        14.6M
        73.3%
        1.9M
        298.0bp
        289.6bp
        10.9M
        9.6M
        10.7M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.2bp
        0.1%
        3.3bp
        BS474
        22.0M
        19.8M
        89.8%
        18.9M
        85.9%
        0.8M
        298.0bp
        289.4bp
        13.3M
        11.8M
        13.1M
        0.1M
        0.0M
        0.1M
        0.9%
        0.1%
        3.2bp
        0.1%
        3.3bp
        BS475
        23.6M
        22.1M
        93.6%
        21.0M
        89.0%
        1.1M
        297.0bp
        290.0bp
        19.4M
        17.6M
        19.2M
        0.2M
        0.0M
        0.0M
        0.8%
        0.1%
        3.0bp
        0.1%
        2.9bp
        BS476
        23.1M
        21.5M
        93.2%
        20.5M
        88.8%
        1.0M
        297.0bp
        290.1bp
        19.4M
        17.5M
        19.1M
        0.2M
        0.0M
        0.1M
        0.8%
        0.1%
        3.0bp
        0.1%
        2.8bp
        BS477
        20.1M
        18.8M
        93.9%
        18.0M
        89.8%
        0.8M
        297.0bp
        290.5bp
        17.4M
        15.6M
        17.1M
        0.2M
        0.0M
        0.0M
        0.8%
        0.1%
        3.0bp
        0.1%
        2.8bp
        BS478
        19.6M
        18.1M
        92.3%
        17.2M
        87.8%
        0.9M
        297.0bp
        289.5bp
        15.4M
        13.8M
        15.2M
        0.2M
        0.0M
        0.0M
        0.8%
        0.1%
        3.0bp
        0.1%
        2.8bp
        BS479
        20.6M
        18.8M
        91.6%
        17.9M
        87.2%
        0.9M
        297.0bp
        289.1bp
        15.2M
        13.7M
        15.0M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.0bp
        0.1%
        2.9bp
        BS480
        21.0M
        19.2M
        91.6%
        18.2M
        86.7%
        1.0M
        297.0bp
        288.8bp
        14.2M
        12.7M
        14.0M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.0bp
        0.1%
        2.9bp
        BS481
        20.9M
        19.2M
        91.6%
        18.3M
        87.3%
        0.9M
        296.0bp
        287.7bp
        13.7M
        12.3M
        13.5M
        0.1M
        0.0M
        0.1M
        0.9%
        0.1%
        3.0bp
        0.1%
        2.8bp
        BS482
        20.4M
        18.7M
        91.5%
        17.7M
        87.0%
        0.9M
        296.0bp
        288.2bp
        14.4M
        12.9M
        14.2M
        0.1M
        0.0M
        0.1M
        0.8%
        0.1%
        3.0bp
        0.1%
        2.8bp
        BS483
        24.3M
        22.3M
        91.7%
        21.2M
        87.2%
        1.1M
        297.0bp
        288.2bp
        16.5M
        14.8M
        16.3M
        0.1M
        0.0M
        0.1M
        0.9%
        0.1%
        3.0bp
        0.1%
        2.9bp
        BS484
        23.1M
        21.2M
        91.6%
        20.1M
        87.1%
        1.0M
        295.0bp
        287.3bp
        17.8M
        16.0M
        17.5M
        0.2M
        0.0M
        0.1M
        0.8%
        0.1%
        3.0bp
        0.1%
        2.9bp
        BS485
        23.6M
        21.8M
        92.4%
        20.8M
        88.3%
        1.0M
        297.0bp
        288.6bp
        17.7M
        15.8M
        17.5M
        0.1M
        0.0M
        0.1M
        0.9%
        0.1%
        3.1bp
        0.1%
        2.9bp
        BS486
        28.0M
        25.7M
        91.9%
        24.5M
        87.4%
        1.3M
        296.0bp
        287.8bp
        19.3M
        17.4M
        19.1M
        0.1M
        0.0M
        0.1M
        0.9%
        0.1%
        3.0bp
        0.1%
        3.0bp

        Alignment Scores

        Created with MultiQC

        Gene Counts

        Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.

        Created with MultiQC

        Cutadapt

        Version: 2.10

        Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.URL: https://cutadapt.readthedocs.ioDOI: 10.14806/ej.17.1.200

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        Created with MultiQC

        Trimmed Sequence Lengths (3')

        This plot shows the number of reads with certain lengths of adapter trimmed for the 3' end.

        Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

        See the cutadapt documentation for more information on how these numbers are generated.

        Created with MultiQC

        Kraken

        Taxonomic classification tool that uses exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.URL: https://ccb.jhu.edu/software/krakenDOI: 10.1186/gb-2014-15-3-r46

        Top taxa

        The number of reads falling into the top 5 taxa across different ranks.

        To make this plot, the percentage of each sample assigned to a given taxa is summed across all samples. The counts for these top 5 taxa are then plotted for each of the 9 different taxa ranks. The unclassified count is always shown across all taxa ranks.

        The total number of reads is approximated by dividing the number of unclassified reads by the percentage of the library that they account for. Note that this is only an approximation, and that kraken percentages don't always add to exactly 100%.

        The category "Other" shows the difference between the above total read count and the sum of the read counts in the top 5 taxa shown + unclassified. This should cover all taxa not in the top 5, +/- any rounding errors.

        Note that any taxon that does not exactly fit a taxon rank (eg. - or G2) is ignored.

        Created with MultiQC

        FastQC

        Version: 0.11.9

        Quality control tool for high throughput sequencing data.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        All samples have sequences of a single length (150bp)

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 0/14 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        CCTCGATCGATTAGTATCTGTCAGCTCCATGTGTCGCCACACTTCCACCT
        2
        140851
        0.0087%
        GGCATGTTACGCGTTGTGCTTTAACACCTCTTGATGAAATACAGCCTGAT
        1
        31636
        0.0020%
        GCATGTTACGCGTTGTGCTTTAACACCTCTTGATGAAATACAGCCTGATA
        1
        28504
        0.0018%
        GCTGATTTAAACCCTTTTTCAAAGTCCCCTTTTTTTGCTGTTTCCTTAAT
        1
        28149
        0.0017%
        CGGCATGTTACGCGTTGTGCTTTAACACCTCTTGATGAAATACAGCCTGA
        1
        27900
        0.0017%
        CTTTCGTCAATGGCAGTAAGGACTTTTCCTTAGAAGTGTAATAAATATCG
        1
        27037
        0.0017%
        TGCTGATTTAAACCCTTTTTCAAAGTCCCCTTTTTTTGCTGTTTCCTTAA
        1
        25826
        0.0016%
        GCTTTTGATTCGAATATCCAATCATAATCTGATTAATACTGACCGCATAT
        1
        25089
        0.0016%
        GCTTTCTCTTCCTCCGGGTACTTAGATGTTTCAGTTCCCCGGGTCTGCCT
        1
        24684
        0.0015%
        GACGGACCGGCTCAGGGAGGGAGACGTTTGCGGGATGGCATAGGAAAGCG
        1
        28416
        0.0018%
        CGGTGGATGCCTTGGCACTAGGAGCCGATGAAGGACGGGACGAACACCGA
        1
        27576
        0.0017%
        GGTGGATGCCTTGGCACTAGGAGCCGATGAAGGACGGGACGAACACCGAT
        1
        25801
        0.0016%
        AGACGGACCGGCTCAGGGAGGGAGACGTTTGCGGGATGGCATAGGAAAGC
        1
        25074
        0.0016%
        CGGACCGGCTCAGGGAGGGAGACGTTTGCGGGATGGCATAGGAAAGCGTG
        1
        24981
        0.0015%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        Cutadapt2.10
        FastQC0.11.9